Chair Anter Isaac said on Sydney radio station SEN1170 that the safety and security of players was FA's top priority as the Socceroos, currently in camp in Doha, prepare to face Qatar on Saturday before travelling to Amman to face Jordan on November 18.
FA chief executive Martin Kugeler and his counterpart at the players' union, Professional Footballers Australia (PFA) boss Beau Busch, have both travelled to Doha amid fears players could pull out of the fixture because of the uncertain situation in Jordan.
Busch said in a statement last week that Socceroos players "have overwhelmingly expressed their view that the Jordan match should be rescheduled or relocated".
Isaac explained the friendlies were arranged with a view to January's Asian Cup - Jordan and Qatar were finalists four years ago - which has since been delayed by 11 months due to conflict in Saudi Arabia.
"Of paramount importance is the safety and security of our players and our staff," Isaac said on Tuesday.
"I know that the team on the ground there is working through things.
"The Qatar game goes ahead and we're hopeful that we can find a resolution for the Jordan game."
The Department of Foreign Affairs and Trade (DFAT) advises Australians to reconsider their need to travel to Jordan following a stabbing in the capital and a gun attack on an orthodox in a church in the country's south over the last month.
Socceroos coach Tony Popovic has already indicated that, if players did withdraw, it would not cloud their selection hopes moving forward.
One possible solution, FA is understood to be considering, is asking to move the Jordan game to Qatar.
That would allay the fears of Socceroos players and save face for the Jordanian FA.
Jordan's November window has already been hampered by Indonesia withdrawing from their friendly which was scheduled to take place this Friday over the security situation.
The uncertainty over the Jordan friendly comes at a time of increased tension between FA and the Socceroos.
Last week AAP revealed the PFA, acting on behalf of Socceroos and Matildas players, has commenced legal action against FA by subpoenaing court documents relating to the revenue share model written into the collective bargaining agreement, which is due to expire next October.
The Socceroos have yet to be paid their match fees from the World Cup, but Isaac guaranteed "all players will be paid in full".
"There's no risk to any entitlements," he said.
"Ideally, we avoid that (legal action) in Australian football, and we want to continue engaging in meaningful dialogue that solves these kinds of issues.
"We recognise the PFA, have a very specific, narrow, important mandate to extract wealth for the elite players.
"Equally, there has to be a recognition that Football Australia's mandate is very different from the PFA's.
"Our mandate is to invest in every level of the game, from the girls and boys that are slipping shin pads into their socks for the very first time, all the way to the Socceroos and Matildas."
